The human large intestine is colonized by a complex community of microorganisms, largely composed of strictly anaerobic bacteria with numerous physiological functions which impact on the host nutrition and health. Among these functions, the fermentation of substrates is of major importance for host health through the production of a wide variety of metabolites. The metabolic functions of the human gut microbiota are correlated with the nature of the substrates available for fermentation in the colon. These substrates are from exogenous (dietary fibers that are mainly plant polysaccharides) and endogenous (produced by the host and represent important source of nitrogen) sources. The metabolites produced from the microbial fermentation process in the gut are mainly absorbed and used by the host. Most of them have health benefits, but some may also have deleterious effects. The gut microbiota should thus be considered in relation to its environment, including dietary food and host factors. The interactions between food, intestinal microbiota and the host are fundamental to the maintenance of homeostasis in the ecosystem. Any disruption of this equilibrium could modify the functionality of the gut microbiota and lead to a pathological state.